OBJECTIVE: To investigate deaths and losses to follow-up in a programme designed to scale up antiretroviral therapy (ART) for HIV-infected children in Côte d'Ivoire. METHODS: Between 2004 and 2007, HIV-exposed children at 19 centres were offered free HIV serum tests (polymerase chain reaction tests in those aged < 18 months) and ART. Computerized monitoring was used to determine: (i) the number of confirmed HIV infections, (ii) losses to the programme (i.e. death or loss to follow-up) before ART, (iii) mortality and loss-to-programme rates during 12 months of ART, and (iv) determinants of mortality and losses to the programme. FINDINGS: The analysis included 3876 ART-naïve children. Of the 1766 with HIV-1 infections (17% aged < 18 months), 124 (7.0%) died, 52 (2.9%) left the programme, 354 (20%) were lost to follow-up before ART, 259 (15%) remained in care without ART, and 977 (55%) started ART (median age: 63 months). The overall mortality rate during ART was significantly higher in the first 3 months than in months 4-12: 32.8 and 6.9 per 100 child-years of follow-up, respectively. Loss-to-programme rates were roughly double mortality rates and followed the same trend with duration of ART. Independent predictors of 12-month mortality on ART were pre-ART weight-for-age z-score < -2, percentage of CD4+ T lymphocytes < 10, World Health Organization HIV/AIDS clinical stage 3 or 4, and blood haemoglobin < 8 g/dl. CONCLUSION: The large-scale programme to scale up paediatric ART in Côte d'Ivoire was effective. However, ART was often given too late, and early mortality and losses to programme before and just after ART initiation were major problems.